Starting phenix.real_space_refine
on Fri Oct 10 17:48:58 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8k9r_36996/10_2025/8k9r_36996_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k9r_36996/10_2025/8k9r_36996.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k9r_36996/10_2025/8k9r_36996.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k9r_36996/10_2025/8k9r_36996.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k9r_36996/10_2025/8k9r_36996_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k9r_36996/10_2025/8k9r_36996_neut.cif"
  }
  resolution = 2.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.104
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      33      5.16       5
     C    4991      2.51       5
     N    1271      2.21       5
     O    1386      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7684
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7487
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 958, 7487
          Classifications: {'peptide': 958}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 896}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 71
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 54
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 41
    Chain: "B"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 24
          Classifications: {'peptide': 4}
          Link IDs: {'TRANS': 3}
    Chain: "A"
      Number of atoms: 155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 155
          Unusual residues: {'05E': 1, 'CLR': 1, 'L9H': 1, 'MAN': 2, 'PA1': 1, 'PLM': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 18
          Unusual residues: {'80Y': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.23, per 1000 atoms: 0.29
  Number of scatterers: 7684
  At special positions: 0
  Unit cell: (78.288, 91.336, 133.276, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      33     16.00
     P       3     15.00
     O    1386      8.00
     N    1271      7.00
     C    4991      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 177 " - pdb=" SG  CYS A 449 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 574 " - pdb=" SG  CYS A 606 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 729 " - pdb=" SG  CYS A 793 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=6, symmetry=0
  Number of additional bonds: simple=6, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 227.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1832

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 5 sheets defined
      47.0% alpha, 14.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 146 through 170
      removed outlier: 3.582A  pdb=" N   VAL A 168 " --> pdb=" O   ILE A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 202
      removed outlier: 3.745A  pdb=" N   SER A 201 " --> pdb=" O   ARG A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 236
    Processing helix  chain 'A' and resid 237 through 251
    Processing helix  chain 'A' and resid 255 through 261
    Processing helix  chain 'A' and resid 281 through 303
      removed outlier: 3.626A  pdb=" N   LEU A 285 " --> pdb=" O   HIS A 281 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   TYR A 303 " --> pdb=" O   ILE A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 337
      removed outlier: 3.851A  pdb=" N   ILE A 331 " --> pdb=" O   SER A 327 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LEU A 337 " --> pdb=" O   ALA A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 384
      removed outlier: 3.507A  pdb=" N   VAL A 369 " --> pdb=" O   ASP A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 391
    Processing helix  chain 'A' and resid 411 through 416
      removed outlier: 3.580A  pdb=" N   SER A 416 " --> pdb=" O   ASP A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 449
      removed outlier: 4.067A  pdb=" N   TRP A 448 " --> pdb=" O   GLN A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 462
    Processing helix  chain 'A' and resid 474 through 487
    Processing helix  chain 'A' and resid 497 through 501
    Processing helix  chain 'A' and resid 610 through 613
    Processing helix  chain 'A' and resid 630 through 634
    Processing helix  chain 'A' and resid 645 through 649
    Processing helix  chain 'A' and resid 675 through 678
      No H-bonds generated for 'chain 'A' and resid 675 through 678'
    Processing helix  chain 'A' and resid 685 through 693
    Processing helix  chain 'A' and resid 777 through 781
      removed outlier: 3.898A  pdb=" N   GLU A 781 " --> pdb=" O   PRO A 778 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 790 through 794
      removed outlier: 3.800A  pdb=" N   CYS A 793 " --> pdb=" O   ASP A 790 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ASN A 794 " --> pdb=" O   PRO A 791 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 790 through 794'
    Processing helix  chain 'A' and resid 805 through 811
    Processing helix  chain 'A' and resid 811 through 817
      removed outlier: 4.208A  pdb=" N   ARG A 815 " --> pdb=" O   LYS A 811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 818 through 822
      removed outlier: 3.528A  pdb=" N   ALA A 821 " --> pdb=" O   THR A 818 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 823 through 843
      removed outlier: 3.715A  pdb=" N   ILE A 827 " --> pdb=" O   PHE A 823 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 847 through 858
      removed outlier: 3.673A  pdb=" N   ARG A 857 " --> pdb=" O   ASP A 853 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   GLN A 858 " --> pdb=" O   LEU A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 858 through 872
    Processing helix  chain 'A' and resid 908 through 912
    Processing helix  chain 'A' and resid 913 through 954
    Processing helix  chain 'A' and resid 985 through 993
      removed outlier: 3.779A  pdb=" N   LEU A 989 " --> pdb=" O   VAL A 985 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   VAL A 990 " --> pdb=" O   LEU A 986 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER A 991 " --> pdb=" O   LEU A 987 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   THR A 992 " --> pdb=" O   PHE A 988 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 995 through 1022
    Processing helix  chain 'A' and resid 1023 through 1061
      removed outlier: 3.540A  pdb=" N   ILE A1043 " --> pdb=" O   LEU A1039 " (cutoff:3.500A)
      Proline residue:  A1045  - end of helix
      Proline residue:  A1049  - end of helix
      removed outlier: 3.504A  pdb=" N   VAL A1053 " --> pdb=" O   PRO A1049 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1067 through 1087
      Proline residue:  A1077  - end of helix
    Processing helix  chain 'A' and resid 1103 through 1125
      removed outlier: 3.678A  pdb=" N   THR A1110 " --> pdb=" O   LEU A1106 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   SER A1111 " --> pdb=" O   ARG A1107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1130 through 1149
      removed outlier: 4.457A  pdb=" N   GLN A1134 " --> pdb=" O   TYR A1130 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 188
      removed outlier: 4.949A  pdb=" N   PHE A 268 " --> pdb=" O   TYR A 208 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   VAL A 222 " --> pdb=" O   ASP A 267 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   PHE A 269 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   VAL A 224 " --> pdb=" O   PHE A 269 " (cutoff:3.500A)
      removed outlier: 7.940A  pdb=" N   VAL A 271 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 7.581A  pdb=" N   PHE A 226 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   VAL A 321 " --> pdb=" O   THR A 349 " (cutoff:3.500A)
      removed outlier: 8.406A  pdb=" N   ILE A 351 " --> pdb=" O   VAL A 321 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   VAL A 323 " --> pdb=" O   ILE A 351 " (cutoff:3.500A)
      removed outlier: 7.767A  pdb=" N   MET A 353 " --> pdb=" O   VAL A 323 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   GLY A 325 " --> pdb=" O   MET A 353 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   ASN A 348 " --> pdb=" O   THR A 397 " (cutoff:3.500A)
      removed outlier: 7.898A  pdb=" N   VAL A 399 " --> pdb=" O   ASN A 348 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ILE A 350 " --> pdb=" O   VAL A 399 " (cutoff:3.500A)
      removed outlier: 7.766A  pdb=" N   ILE A 401 " --> pdb=" O   ILE A 350 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   THR A 352 " --> pdb=" O   ILE A 401 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   LEU A 398 " --> pdb=" O   PHE A 427 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   VAL A 429 " --> pdb=" O   LEU A 398 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   SER A 400 " --> pdb=" O   VAL A 429 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 540
    Processing sheet with id=AA3, first strand: chain 'A' and resid 523 through 528
      removed outlier: 4.013A  pdb=" N   VAL A 524 " --> pdb=" O   VAL A 668 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   VAL A 668 " --> pdb=" O   VAL A 524 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   ARG A 526 " --> pdb=" O   GLY A 666 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   GLY A 666 " --> pdb=" O   ARG A 526 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 679 through 681
      removed outlier: 6.685A  pdb=" N   HIS A 680 " --> pdb=" O   ARG A 709 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   GLU A 749 " --> pdb=" O   LEU A 744 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 694 through 698
      removed outlier: 4.577A  pdb=" N   ALA A 719 " --> pdb=" O   ASP A 804 " (cutoff:3.500A)

    375 hydrogen bonds defined for protein.
    1041 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.26

  Time building geometry restraints manager: 1.06 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.17 -     1.30: 1171
        1.30 -     1.43: 2107
        1.43 -     1.56: 4545
        1.56 -     1.69: 6
        1.69 -     1.82: 55
  Bond restraints: 7884
  Sorted by residual:
  bond pdb=" C   LYS A 235 "
       pdb=" O   LYS A 235 "
    ideal  model  delta    sigma   weight residual
    1.235  1.171  0.064 1.38e-02 5.25e+03 2.14e+01
  bond pdb=" O75 80Y B 101 "
       pdb=" P76 80Y B 101 "
    ideal  model  delta    sigma   weight residual
    1.646  1.559  0.087 2.00e-02 2.50e+03 1.89e+01
  bond pdb=" OA5 L9H A1505 "
       pdb=" PA6 L9H A1505 "
    ideal  model  delta    sigma   weight residual
    1.651  1.566  0.085 2.00e-02 2.50e+03 1.80e+01
  bond pdb=" CA  SER A 327 "
       pdb=" CB  SER A 327 "
    ideal  model  delta    sigma   weight residual
    1.530  1.469  0.061 1.53e-02 4.27e+03 1.58e+01
  bond pdb=" C   SER A 327 "
       pdb=" O   SER A 327 "
    ideal  model  delta    sigma   weight residual
    1.243  1.210  0.033 9.50e-03 1.11e+04 1.21e+01
  ... (remaining 7879 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 10304
        1.93 -     3.85: 394
        3.85 -     5.78: 54
        5.78 -     7.71: 4
        7.71 -     9.64: 2
  Bond angle restraints: 10758
  Sorted by residual:
  angle pdb=" N   THR B   2 "
        pdb=" CA  THR B   2 "
        pdb=" C   THR B   2 "
      ideal   model   delta    sigma   weight residual
     114.56  106.82    7.74 1.27e+00 6.20e-01 3.72e+01
  angle pdb=" N   LYS A 235 "
        pdb=" CA  LYS A 235 "
        pdb=" C   LYS A 235 "
      ideal   model   delta    sigma   weight residual
     113.17  106.37    6.80 1.26e+00 6.30e-01 2.92e+01
  angle pdb=" C   THR B   2 "
        pdb=" CA  THR B   2 "
        pdb=" CB  THR B   2 "
      ideal   model   delta    sigma   weight residual
     109.13  115.48   -6.35 1.56e+00 4.11e-01 1.66e+01
  angle pdb=" N   PRO A 703 "
        pdb=" CA  PRO A 703 "
        pdb=" C   PRO A 703 "
      ideal   model   delta    sigma   weight residual
     111.22  105.77    5.45 1.40e+00 5.10e-01 1.51e+01
  angle pdb=" CA  LEU A 902 "
        pdb=" C   LEU A 902 "
        pdb=" O   LEU A 902 "
      ideal   model   delta    sigma   weight residual
     121.11  116.87    4.24 1.13e+00 7.83e-01 1.41e+01
  ... (remaining 10753 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.91: 4740
       35.91 -    71.82: 99
       71.82 -   107.73: 9
      107.73 -   143.63: 3
      143.63 -   179.54: 4
  Dihedral angle restraints: 4855
    sinusoidal: 2033
      harmonic: 2822
  Sorted by residual:
  dihedral pdb=" C81 05E A1503 "
           pdb=" O82 05E A1503 "
           pdb=" P83 05E A1503 "
           pdb=" O84 05E A1503 "
      ideal   model   delta sinusoidal    sigma   weight residual
     248.92   69.38  179.54     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C73 80Y B 101 "
           pdb=" C74 80Y B 101 "
           pdb=" O75 80Y B 101 "
           pdb=" P76 80Y B 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
      94.72  -86.64 -178.64     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C81 05E A1503 "
           pdb=" O82 05E A1503 "
           pdb=" P83 05E A1503 "
           pdb=" O88 05E A1503 "
      ideal   model   delta sinusoidal    sigma   weight residual
       5.56 -177.67 -176.77     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 4852 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 843
       0.045 -    0.090: 307
       0.090 -    0.136: 95
       0.136 -    0.181: 14
       0.181 -    0.226: 11
  Chirality restraints: 1270
  Sorted by residual:
  chirality pdb=" C2  MAN A1502 "
            pdb=" C1  MAN A1502 "
            pdb=" C3  MAN A1502 "
            pdb=" O2  MAN A1502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.52    2.74   -0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CA  ILE A 577 "
            pdb=" N   ILE A 577 "
            pdb=" C   ILE A 577 "
            pdb=" CB  ILE A 577 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  PHE A 622 "
            pdb=" N   PHE A 622 "
            pdb=" C   PHE A 622 "
            pdb=" CB  PHE A 622 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.09e+00
  ... (remaining 1267 not shown)

  Planarity restraints: 1330
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 379 "   -0.027 2.00e-02 2.50e+03   2.46e-02 1.51e+01
        pdb=" CG  TRP A 379 "    0.066 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 379 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 379 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 379 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 379 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 379 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 379 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 379 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 379 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A1135 "    0.016 2.00e-02 2.50e+03   2.01e-02 7.04e+00
        pdb=" CG  PHE A1135 "   -0.045 2.00e-02 2.50e+03
        pdb=" CD1 PHE A1135 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 PHE A1135 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE A1135 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE A1135 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE A1135 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 234 "   -0.011 2.00e-02 2.50e+03   2.27e-02 5.13e+00
        pdb=" C   TYR A 234 "    0.039 2.00e-02 2.50e+03
        pdb=" O   TYR A 234 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   LYS A 235 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1327 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1460
        2.77 -     3.30: 7201
        3.30 -     3.83: 13128
        3.83 -     4.37: 16224
        4.37 -     4.90: 27351
  Nonbonded interactions: 65364
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 178 "
            pdb=" OE2 GLU A 634 "
     model   vdw
     2.233 3.120
  nonbonded pdb=" O   ASP A 901 "
            pdb=" OG  SER A1127 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" NH1 ARG A 741 "
            pdb=" OE1 GLN A 786 "
     model   vdw
     2.310 3.120
  nonbonded pdb=" NH1 ARG A 522 "
            pdb=" OE2 GLU A 671 "
     model   vdw
     2.353 3.120
  nonbonded pdb=" OG  SER A 716 "
            pdb=" NH2 ARG A 815 "
     model   vdw
     2.381 3.120
  ... (remaining 65359 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     9.140
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.102   7893  Z= 0.446
  Angle     :  0.818   9.635  10764  Z= 0.494
  Chirality :  0.053   0.226   1270
  Planarity :  0.005   0.053   1330
  Dihedral  : 16.147 179.543   3014
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  1.09 %
    Favored  : 97.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.27), residues: 952
  helix:  0.78 (0.26), residues: 372
  sheet:  1.26 (0.45), residues: 141
  loop : -0.22 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 359 
 TYR   0.014   0.002   TYR A 372 
 PHE   0.045   0.002   PHE A1135 
 TRP   0.066   0.003   TRP A 379 
 HIS   0.007   0.001   HIS A 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00872 ( 7884)
  covalent geometry    : angle       0.81706 (10758)
  SS BOND              : bond        0.00972 (    3)
  SS BOND              : angle       1.41835 (    6)
  hydrogen bonds       : bond        0.16834 (  375)
  hydrogen bonds       : angle       7.22253 ( 1041)
  Misc. bond           : bond        0.04522 (    6)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 123
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A  220 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7918 (mtm-85)
REVERT: A  275 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7669 (mm-30)
REVERT: A  386 LYS cc_start: 0.8396 (ttmt) cc_final: 0.8136 (mptt)
REVERT: A  387 TRP cc_start: 0.7629 (m-90) cc_final: 0.7258 (m100)
REVERT: A  570 GLU cc_start: 0.7979 (tt0) cc_final: 0.7726 (tt0)
REVERT: A  630 ARG cc_start: 0.7514 (mtp-110) cc_final: 0.7305 (mtm-85)
REVERT: A  674 ASP cc_start: 0.8375 (m-30) cc_final: 0.8034 (m-30)
REVERT: A  687 ARG cc_start: 0.7344 (ttm110) cc_final: 0.7063 (ttp80)
REVERT: A  800 ASP cc_start: 0.7751 (m-30) cc_final: 0.7548 (m-30)
REVERT: A  903 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8000 (tt)
REVERT: A 1059 SER cc_start: 0.8784 (m) cc_final: 0.8489 (p)
REVERT: A 1083 GLU cc_start: 0.7314 (tp30) cc_final: 0.7049 (tm-30)
  outliers start: 11
  outliers final: 1
  residues processed: 131
  average time/residue: 0.7006
  time to fit residues: 95.9278
Evaluate side-chains
  95 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 92
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 ARG
Chi-restraints excluded: chain A residue  903 LEU
Chi-restraints excluded: chain B residue    2 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    7.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 230 ASN
A1026 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.127666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.098724 restraints weight = 9728.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 1.98
r_work: 0.3107 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.1153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7893  Z= 0.141
  Angle     :  0.556   6.935  10764  Z= 0.283
  Chirality :  0.042   0.140   1270
  Planarity :  0.005   0.046   1330
  Dihedral  : 14.154 176.762   1315
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  8.36 %
    Favored  : 90.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.28), residues: 952
  helix:  1.62 (0.27), residues: 371
  sheet:  1.12 (0.44), residues: 147
  loop :  0.09 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 453 
 TYR   0.009   0.001   TYR A 996 
 PHE   0.019   0.001   PHE A 826 
 TRP   0.017   0.001   TRP A 379 
 HIS   0.002   0.001   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 7884)
  covalent geometry    : angle       0.55593 (10758)
  SS BOND              : bond        0.00195 (    3)
  SS BOND              : angle       0.35807 (    6)
  hydrogen bonds       : bond        0.04503 (  375)
  hydrogen bonds       : angle       5.37548 ( 1041)
  Misc. bond           : bond        0.00145 (    6)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7726 (mm-30)
REVERT: A  386 LYS cc_start: 0.8483 (ttmt) cc_final: 0.8090 (mptt)
REVERT: A  570 GLU cc_start: 0.8530 (tt0) cc_final: 0.8326 (tt0)
REVERT: A  674 ASP cc_start: 0.8590 (m-30) cc_final: 0.8149 (m-30)
REVERT: A 1083 GLU cc_start: 0.7845 (tp30) cc_final: 0.7465 (tm-30)
  outliers start: 11
  outliers final: 6
  residues processed: 106
  average time/residue: 0.7459
  time to fit residues: 82.8790
Evaluate side-chains
  91 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  575 SER
Chi-restraints excluded: chain A residue  725 SER
Chi-restraints excluded: chain A residue  903 LEU
Chi-restraints excluded: chain A residue  942 VAL
Chi-restraints excluded: chain B residue    2 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 54 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 20 optimal weight:    0.4980
   chunk 48 optimal weight:    0.0870
   overall best weight:    0.6158

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 898 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.128244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.099417 restraints weight = 9678.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 1.97
r_work: 0.3141 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.1513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7893  Z= 0.115
  Angle     :  0.496   6.179  10764  Z= 0.252
  Chirality :  0.041   0.155   1270
  Planarity :  0.004   0.044   1330
  Dihedral  : 12.959 178.493   1311
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 11.64 %
    Favored  : 87.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.28), residues: 952
  helix:  2.08 (0.27), residues: 370
  sheet:  0.95 (0.43), residues: 158
  loop :  0.25 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 723 
 TYR   0.011   0.001   TYR A 996 
 PHE   0.015   0.001   PHE A 826 
 TRP   0.011   0.001   TRP A 448 
 HIS   0.002   0.000   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 7884)
  covalent geometry    : angle       0.49622 (10758)
  SS BOND              : bond        0.00080 (    3)
  SS BOND              : angle       0.56803 (    6)
  hydrogen bonds       : bond        0.03858 (  375)
  hydrogen bonds       : angle       4.93944 ( 1041)
  Misc. bond           : bond        0.00051 (    6)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7747 (mm-30)
REVERT: A  386 LYS cc_start: 0.8490 (ttmt) cc_final: 0.8092 (mptt)
REVERT: A  527 GLU cc_start: 0.7122 (pm20) cc_final: 0.6641 (mp0)
REVERT: A  674 ASP cc_start: 0.8496 (m-30) cc_final: 0.8150 (m-30)
REVERT: A  687 ARG cc_start: 0.7768 (ttm110) cc_final: 0.7108 (ttt180)
REVERT: A  837 GLN cc_start: 0.8083 (mt0) cc_final: 0.7853 (mt0)
REVERT: A 1083 GLU cc_start: 0.7835 (tp30) cc_final: 0.7553 (tm-30)
  outliers start: 9
  outliers final: 6
  residues processed: 97
  average time/residue: 0.6915
  time to fit residues: 70.3482
Evaluate side-chains
  91 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  442 ASP
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  575 SER
Chi-restraints excluded: chain A residue  612 ASP
Chi-restraints excluded: chain A residue  903 LEU
Chi-restraints excluded: chain A residue  942 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 90 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 79 optimal weight:    9.9990
   chunk 57 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 21 optimal weight:    0.4980
   chunk 18 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    1.6586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 758 GLN
A 898 HIS
A1057 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.125815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.096605 restraints weight = 9920.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 2.00
r_work: 0.3079 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.1463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   7893  Z= 0.201
  Angle     :  0.547   6.206  10764  Z= 0.278
  Chirality :  0.043   0.152   1270
  Planarity :  0.005   0.044   1330
  Dihedral  : 12.553 174.951   1310
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 12.85 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.28), residues: 952
  helix:  2.04 (0.27), residues: 371
  sheet:  0.99 (0.42), residues: 163
  loop :  0.28 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 723 
 TYR   0.014   0.001   TYR A 996 
 PHE   0.022   0.001   PHE A 826 
 TRP   0.010   0.001   TRP A 448 
 HIS   0.003   0.001   HIS A 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 7884)
  covalent geometry    : angle       0.54712 (10758)
  SS BOND              : bond        0.00182 (    3)
  SS BOND              : angle       0.36941 (    6)
  hydrogen bonds       : bond        0.04434 (  375)
  hydrogen bonds       : angle       4.96041 ( 1041)
  Misc. bond           : bond        0.00085 (    6)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7873 (mm-30)
REVERT: A  386 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8126 (mptt)
REVERT: A  527 GLU cc_start: 0.7208 (pm20) cc_final: 0.6676 (mp0)
REVERT: A  572 MET cc_start: 0.8737 (ptp) cc_final: 0.8413 (mtm)
REVERT: A  674 ASP cc_start: 0.8574 (m-30) cc_final: 0.8226 (m-30)
REVERT: A  687 ARG cc_start: 0.7765 (ttm110) cc_final: 0.7113 (ttt180)
REVERT: A  723 ARG cc_start: 0.8389 (mmm-85) cc_final: 0.8142 (mtp85)
REVERT: A  899 GLN cc_start: 0.8496 (pt0) cc_final: 0.8243 (pt0)
REVERT: A 1083 GLU cc_start: 0.7928 (tp30) cc_final: 0.7592 (tm-30)
  outliers start: 12
  outliers final: 8
  residues processed: 93
  average time/residue: 0.7837
  time to fit residues: 76.3220
Evaluate side-chains
  90 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  575 SER
Chi-restraints excluded: chain A residue  725 SER
Chi-restraints excluded: chain A residue  762 SER
Chi-restraints excluded: chain A residue  903 LEU
Chi-restraints excluded: chain A residue  942 VAL
Chi-restraints excluded: chain A residue 1021 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 85 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 91 optimal weight:    1.9990
   chunk 38 optimal weight:    0.1980
   chunk 14 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 758 GLN
A 898 HIS
A 907 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.127355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.098139 restraints weight = 9802.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 1.99
r_work: 0.3126 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3026 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.1682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7893  Z= 0.116
  Angle     :  0.486   6.293  10764  Z= 0.248
  Chirality :  0.041   0.126   1270
  Planarity :  0.004   0.042   1330
  Dihedral  : 12.236 175.827   1310
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 13.70 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.28), residues: 952
  helix:  2.19 (0.27), residues: 370
  sheet:  0.87 (0.42), residues: 164
  loop :  0.31 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 702 
 TYR   0.010   0.001   TYR A 996 
 PHE   0.016   0.001   PHE A 826 
 TRP   0.011   0.001   TRP A 448 
 HIS   0.002   0.000   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 7884)
  covalent geometry    : angle       0.48643 (10758)
  SS BOND              : bond        0.00061 (    3)
  SS BOND              : angle       0.35934 (    6)
  hydrogen bonds       : bond        0.03713 (  375)
  hydrogen bonds       : angle       4.78613 ( 1041)
  Misc. bond           : bond        0.00040 (    6)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7852 (mm-30)
REVERT: A  386 LYS cc_start: 0.8466 (ttmt) cc_final: 0.8101 (mptt)
REVERT: A  527 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6729 (mp0)
REVERT: A  572 MET cc_start: 0.8708 (ptp) cc_final: 0.8348 (mtm)
REVERT: A  575 SER cc_start: 0.7846 (OUTLIER) cc_final: 0.7433 (m)
REVERT: A  674 ASP cc_start: 0.8595 (m-30) cc_final: 0.8242 (m-30)
REVERT: A  687 ARG cc_start: 0.7838 (ttm110) cc_final: 0.7215 (ttp-170)
REVERT: A  723 ARG cc_start: 0.8404 (mmm-85) cc_final: 0.8142 (mtp85)
REVERT: A  837 GLN cc_start: 0.8050 (mt0) cc_final: 0.7842 (mt0)
REVERT: A  899 GLN cc_start: 0.8528 (pt0) cc_final: 0.8275 (pt0)
REVERT: A 1083 GLU cc_start: 0.7892 (tp30) cc_final: 0.7613 (tm-30)
  outliers start: 11
  outliers final: 6
  residues processed: 94
  average time/residue: 0.7856
  time to fit residues: 77.3204
Evaluate side-chains
  90 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  442 ASP
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain A residue  575 SER
Chi-restraints excluded: chain A residue  762 SER
Chi-restraints excluded: chain A residue  903 LEU
Chi-restraints excluded: chain A residue  942 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 48 optimal weight:    0.2980
   chunk 52 optimal weight:    5.9990
   chunk 31 optimal weight:    0.8980
   chunk 78 optimal weight:    0.8980
   chunk 82 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0980
   chunk 58 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 898 HIS
A 907 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.127183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.097984 restraints weight = 9771.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 1.99
r_work: 0.3122 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.1751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7893  Z= 0.125
  Angle     :  0.488   6.215  10764  Z= 0.248
  Chirality :  0.041   0.125   1270
  Planarity :  0.004   0.041   1330
  Dihedral  : 11.989 174.761   1310
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.70 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.71 (0.28), residues: 952
  helix:  2.17 (0.27), residues: 372
  sheet:  0.87 (0.40), residues: 177
  loop :  0.37 (0.33), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 723 
 TYR   0.010   0.001   TYR A 996 
 PHE   0.017   0.001   PHE A 826 
 TRP   0.010   0.001   TRP A 448 
 HIS   0.002   0.000   HIS A1056 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 7884)
  covalent geometry    : angle       0.48806 (10758)
  SS BOND              : bond        0.00113 (    3)
  SS BOND              : angle       0.30600 (    6)
  hydrogen bonds       : bond        0.03730 (  375)
  hydrogen bonds       : angle       4.73096 ( 1041)
  Misc. bond           : bond        0.00052 (    6)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7838 (mm-30)
REVERT: A  386 LYS cc_start: 0.8468 (ttmt) cc_final: 0.8091 (mptt)
REVERT: A  527 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6710 (mp0)
REVERT: A  572 MET cc_start: 0.8725 (ptp) cc_final: 0.8383 (mtm)
REVERT: A  575 SER cc_start: 0.7811 (OUTLIER) cc_final: 0.7398 (m)
REVERT: A  674 ASP cc_start: 0.8576 (m-30) cc_final: 0.8230 (m-30)
REVERT: A  687 ARG cc_start: 0.7825 (ttm110) cc_final: 0.7177 (ttp-170)
REVERT: A  723 ARG cc_start: 0.8391 (mmm-85) cc_final: 0.8135 (mtp85)
REVERT: A  837 GLN cc_start: 0.8056 (mt0) cc_final: 0.7825 (mt0)
REVERT: A  899 GLN cc_start: 0.8584 (pt0) cc_final: 0.8316 (pt0)
REVERT: A 1073 PHE cc_start: 0.7804 (m-10) cc_final: 0.6326 (t80)
REVERT: A 1083 GLU cc_start: 0.7945 (tp30) cc_final: 0.7590 (tm-30)
  outliers start: 13
  outliers final: 8
  residues processed: 93
  average time/residue: 0.8008
  time to fit residues: 77.8478
Evaluate side-chains
  91 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain A residue  575 SER
Chi-restraints excluded: chain A residue  607 THR
Chi-restraints excluded: chain A residue  725 SER
Chi-restraints excluded: chain A residue  762 SER
Chi-restraints excluded: chain A residue  903 LEU
Chi-restraints excluded: chain A residue  942 VAL
Chi-restraints excluded: chain A residue 1021 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 83 optimal weight:    4.9990
   chunk 80 optimal weight:    0.0870
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0670
   chunk 58 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.0298

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 348 ASN
A 898 HIS
A 907 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.127487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.098831 restraints weight = 9707.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 1.96
r_work: 0.3120 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7893  Z= 0.138
  Angle     :  0.498   6.211  10764  Z= 0.253
  Chirality :  0.041   0.129   1270
  Planarity :  0.004   0.040   1330
  Dihedral  : 11.816 172.956   1310
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 13.58 %
    Favored  : 84.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.71 (0.28), residues: 952
  helix:  2.16 (0.27), residues: 372
  sheet:  0.87 (0.40), residues: 177
  loop :  0.39 (0.33), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 723 
 TYR   0.011   0.001   TYR A 996 
 PHE   0.018   0.001   PHE A 826 
 TRP   0.010   0.001   TRP A 448 
 HIS   0.002   0.000   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 7884)
  covalent geometry    : angle       0.49783 (10758)
  SS BOND              : bond        0.00104 (    3)
  SS BOND              : angle       0.33523 (    6)
  hydrogen bonds       : bond        0.03826 (  375)
  hydrogen bonds       : angle       4.73543 ( 1041)
  Misc. bond           : bond        0.00058 (    6)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7874 (mm-30)
REVERT: A  386 LYS cc_start: 0.8470 (ttmt) cc_final: 0.8114 (mptt)
REVERT: A  441 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8014 (mtm)
REVERT: A  527 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6711 (mp0)
REVERT: A  572 MET cc_start: 0.8770 (ptp) cc_final: 0.8416 (mtm)
REVERT: A  575 SER cc_start: 0.7864 (OUTLIER) cc_final: 0.7454 (m)
REVERT: A  674 ASP cc_start: 0.8570 (m-30) cc_final: 0.8228 (m-30)
REVERT: A  687 ARG cc_start: 0.7871 (ttm110) cc_final: 0.7234 (ttp-170)
REVERT: A  723 ARG cc_start: 0.8408 (mmm-85) cc_final: 0.8156 (mtp85)
REVERT: A  837 GLN cc_start: 0.8087 (mt0) cc_final: 0.7858 (mt0)
REVERT: A 1073 PHE cc_start: 0.7818 (m-10) cc_final: 0.6355 (t80)
REVERT: A 1083 GLU cc_start: 0.7958 (tp30) cc_final: 0.7576 (tm-30)
  outliers start: 16
  outliers final: 9
  residues processed: 92
  average time/residue: 0.8204
  time to fit residues: 78.9525
Evaluate side-chains
  95 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ARG
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  441 MET
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain A residue  575 SER
Chi-restraints excluded: chain A residue  607 THR
Chi-restraints excluded: chain A residue  725 SER
Chi-restraints excluded: chain A residue  762 SER
Chi-restraints excluded: chain A residue  903 LEU
Chi-restraints excluded: chain A residue  942 VAL
Chi-restraints excluded: chain A residue 1021 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 92 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0770
   chunk 12 optimal weight:    6.9990
   chunk 94 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.6738

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 907 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.127971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.098941 restraints weight = 9745.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 1.99
r_work: 0.3140 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7893  Z= 0.110
  Angle     :  0.476   6.292  10764  Z= 0.242
  Chirality :  0.040   0.126   1270
  Planarity :  0.004   0.039   1330
  Dihedral  : 11.602 172.449   1310
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 13.70 %
    Favored  : 84.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.76 (0.28), residues: 952
  helix:  2.23 (0.27), residues: 372
  sheet:  0.74 (0.40), residues: 180
  loop :  0.46 (0.33), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 603 
 TYR   0.009   0.001   TYR A 996 
 PHE   0.015   0.001   PHE A 826 
 TRP   0.011   0.001   TRP A 448 
 HIS   0.002   0.000   HIS A1056 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 7884)
  covalent geometry    : angle       0.47655 (10758)
  SS BOND              : bond        0.00098 (    3)
  SS BOND              : angle       0.30633 (    6)
  hydrogen bonds       : bond        0.03540 (  375)
  hydrogen bonds       : angle       4.65766 ( 1041)
  Misc. bond           : bond        0.00041 (    6)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8444 (mt-10) cc_final: 0.7869 (mm-30)
REVERT: A  386 LYS cc_start: 0.8444 (ttmt) cc_final: 0.8092 (mptt)
REVERT: A  527 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6720 (mp0)
REVERT: A  572 MET cc_start: 0.8743 (ptp) cc_final: 0.8385 (mtm)
REVERT: A  575 SER cc_start: 0.7844 (OUTLIER) cc_final: 0.7454 (m)
REVERT: A  674 ASP cc_start: 0.8568 (m-30) cc_final: 0.8230 (m-30)
REVERT: A  687 ARG cc_start: 0.7864 (ttm110) cc_final: 0.7223 (ttp-170)
REVERT: A  723 ARG cc_start: 0.8412 (mmm-85) cc_final: 0.8159 (mtp85)
REVERT: A  837 GLN cc_start: 0.8106 (mt0) cc_final: 0.7865 (mt0)
REVERT: A 1073 PHE cc_start: 0.7789 (m-10) cc_final: 0.6349 (t80)
REVERT: A 1083 GLU cc_start: 0.7908 (tp30) cc_final: 0.7556 (tm-30)
  outliers start: 14
  outliers final: 8
  residues processed: 94
  average time/residue: 0.7984
  time to fit residues: 78.6169
Evaluate side-chains
  94 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ARG
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain A residue  575 SER
Chi-restraints excluded: chain A residue  607 THR
Chi-restraints excluded: chain A residue  725 SER
Chi-restraints excluded: chain A residue  762 SER
Chi-restraints excluded: chain A residue  942 VAL
Chi-restraints excluded: chain A residue 1021 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9980
   chunk 90 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 69 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0570
   chunk 27 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   overall best weight:    0.6898

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 758 GLN
A 899 GLN
A 907 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.128369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.099237 restraints weight = 9737.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 1.99
r_work: 0.3137 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.1943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7893  Z= 0.112
  Angle     :  0.478   6.108  10764  Z= 0.243
  Chirality :  0.040   0.125   1270
  Planarity :  0.004   0.039   1330
  Dihedral  : 11.318 171.097   1308
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 13.45 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.28), residues: 952
  helix:  2.35 (0.27), residues: 366
  sheet:  0.68 (0.40), residues: 182
  loop :  0.49 (0.33), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 603 
 TYR   0.009   0.001   TYR A 996 
 PHE   0.016   0.001   PHE A 826 
 TRP   0.010   0.001   TRP A 448 
 HIS   0.002   0.000   HIS A1056 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 7884)
  covalent geometry    : angle       0.47814 (10758)
  SS BOND              : bond        0.00086 (    3)
  SS BOND              : angle       0.31655 (    6)
  hydrogen bonds       : bond        0.03517 (  375)
  hydrogen bonds       : angle       4.61513 ( 1041)
  Misc. bond           : bond        0.00041 (    6)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8456 (mt-10) cc_final: 0.7872 (mm-30)
REVERT: A  386 LYS cc_start: 0.8481 (ttmt) cc_final: 0.8123 (mptt)
REVERT: A  527 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6729 (mp0)
REVERT: A  572 MET cc_start: 0.8736 (ptp) cc_final: 0.8394 (mtm)
REVERT: A  575 SER cc_start: 0.7826 (OUTLIER) cc_final: 0.7436 (m)
REVERT: A  674 ASP cc_start: 0.8565 (m-30) cc_final: 0.8224 (m-30)
REVERT: A  687 ARG cc_start: 0.7845 (ttm110) cc_final: 0.7268 (ttp-170)
REVERT: A  723 ARG cc_start: 0.8422 (mmm-85) cc_final: 0.8175 (mtp85)
REVERT: A  837 GLN cc_start: 0.8087 (mt0) cc_final: 0.7830 (mt0)
REVERT: A 1073 PHE cc_start: 0.7792 (m-10) cc_final: 0.6333 (t80)
REVERT: A 1083 GLU cc_start: 0.7906 (tp30) cc_final: 0.7542 (tm-30)
  outliers start: 14
  outliers final: 8
  residues processed: 95
  average time/residue: 0.8278
  time to fit residues: 82.2334
Evaluate side-chains
  97 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ARG
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain A residue  575 SER
Chi-restraints excluded: chain A residue  607 THR
Chi-restraints excluded: chain A residue  725 SER
Chi-restraints excluded: chain A residue  762 SER
Chi-restraints excluded: chain A residue  942 VAL
Chi-restraints excluded: chain A residue 1021 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 52 optimal weight:    0.5980
   chunk 72 optimal weight:    0.4980
   overall best weight:    1.6186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 907 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.126238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.097198 restraints weight = 9748.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 1.98
r_work: 0.3089 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7893  Z= 0.192
  Angle     :  0.538   6.289  10764  Z= 0.272
  Chirality :  0.043   0.152   1270
  Planarity :  0.004   0.038   1330
  Dihedral  : 11.331 167.608   1308
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 13.94 %
    Favored  : 84.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.73 (0.28), residues: 952
  helix:  2.21 (0.27), residues: 366
  sheet:  0.76 (0.40), residues: 180
  loop :  0.46 (0.33), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 603 
 TYR   0.013   0.001   TYR A 996 
 PHE   0.023   0.001   PHE A 826 
 TRP   0.008   0.001   TRP A 448 
 HIS   0.002   0.001   HIS A 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 7884)
  covalent geometry    : angle       0.53833 (10758)
  SS BOND              : bond        0.00163 (    3)
  SS BOND              : angle       0.32325 (    6)
  hydrogen bonds       : bond        0.04200 (  375)
  hydrogen bonds       : angle       4.78153 ( 1041)
  Misc. bond           : bond        0.00084 (    6)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A  275 GLU cc_start: 0.8499 (mt-10) cc_final: 0.7922 (mm-30)
REVERT: A  386 LYS cc_start: 0.8497 (ttmt) cc_final: 0.8146 (mptt)
REVERT: A  527 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6790 (mp0)
REVERT: A  572 MET cc_start: 0.8798 (ptp) cc_final: 0.8486 (mtm)
REVERT: A  575 SER cc_start: 0.7828 (OUTLIER) cc_final: 0.7427 (m)
REVERT: A  674 ASP cc_start: 0.8573 (m-30) cc_final: 0.8228 (m-30)
REVERT: A  687 ARG cc_start: 0.7896 (ttm110) cc_final: 0.7258 (ttp-170)
REVERT: A  723 ARG cc_start: 0.8458 (mmm-85) cc_final: 0.8178 (mtp85)
REVERT: A  837 GLN cc_start: 0.8095 (mt0) cc_final: 0.7881 (mt0)
REVERT: A 1073 PHE cc_start: 0.7795 (m-10) cc_final: 0.6357 (t80)
REVERT: A 1083 GLU cc_start: 0.7963 (tp30) cc_final: 0.7561 (tm-30)
  outliers start: 14
  outliers final: 9
  residues processed: 94
  average time/residue: 0.8372
  time to fit residues: 82.2632
Evaluate side-chains
  96 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ARG
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain A residue  575 SER
Chi-restraints excluded: chain A residue  607 THR
Chi-restraints excluded: chain A residue  725 SER
Chi-restraints excluded: chain A residue  762 SER
Chi-restraints excluded: chain A residue  903 LEU
Chi-restraints excluded: chain A residue  942 VAL
Chi-restraints excluded: chain A residue 1021 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 83 optimal weight:    0.0770
   chunk 86 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0570
   chunk 0 optimal weight:    4.9990
   chunk 93 optimal weight:    0.6980
   overall best weight:    0.4856

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 907 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.129263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.100866 restraints weight = 9674.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 1.94
r_work: 0.3154 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3053 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7893  Z= 0.102
  Angle     :  0.495   8.430  10764  Z= 0.253
  Chirality :  0.040   0.128   1270
  Planarity :  0.004   0.039   1330
  Dihedral  : 11.196 167.740   1308
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 14.30 %
    Favored  : 84.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.78 (0.28), residues: 952
  helix:  2.26 (0.27), residues: 372
  sheet:  0.63 (0.40), residues: 183
  loop :  0.51 (0.33), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 603 
 TYR   0.008   0.001   TYR A 996 
 PHE   0.014   0.001   PHE A 826 
 TRP   0.012   0.001   TRP A 448 
 HIS   0.001   0.000   HIS A1056 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 7884)
  covalent geometry    : angle       0.49075 (10758)
  SS BOND              : bond        0.00577 (    3)
  SS BOND              : angle       2.66650 (    6)
  hydrogen bonds       : bond        0.03468 (  375)
  hydrogen bonds       : angle       4.61637 ( 1041)
  Misc. bond           : bond        0.00027 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3157.65 seconds
wall clock time: 54 minutes 33.33 seconds (3273.33 seconds total)